Markdown was designed to easily be able to convert to HTML so that's not going to be a problem going forward. (Just make sure to keep your old Markdown originals around, too.)
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I've got backups, so losing my originals shouldn't be a problem. Besides, I like using makefiles to rebuild my pages when I change the sources.
The problem I've been having is using m4 macros and includes with markdown. When I run m4 before the markdown converter, the resulting HTML comes out mangled.
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